BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 039206
         (645 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|2PMP|A Chain A, Structure Of 2c-Methyl-D-Erythritol 2,4-Cyclodiphosphate
           Synthase From The Isoprenoid Biosynthetic Pathway Of
           Arabidopsis Thaliana
          Length = 160

 Score = 29.6 bits (65), Expect = 5.7,   Method: Composition-based stats.
 Identities = 14/37 (37%), Positives = 23/37 (62%)

Query: 72  KQSSSSIDVDMKIRLLDERAKEIENKESELVLVEKKI 108
           K ++SS+ +   +RL+DE   EI N ++ L+L   KI
Sbjct: 72  KGAASSVFIKEAVRLMDEAGYEIGNLDATLILQRPKI 108


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.316    0.132    0.359 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,073,687
Number of Sequences: 62578
Number of extensions: 526490
Number of successful extensions: 1938
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 43
Number of HSP's that attempted gapping in prelim test: 1889
Number of HSP's gapped (non-prelim): 84
length of query: 645
length of database: 14,973,337
effective HSP length: 105
effective length of query: 540
effective length of database: 8,402,647
effective search space: 4537429380
effective search space used: 4537429380
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)